x_vaish kraken v bracken
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report
generated on 2024-05-29, 13:37 CEST
based on data in:
/proj/applied_bioinformatics/users/x_vaish/MedBioinfo/analyses/kraken2
General Statistics
| Sample Name | % Corynebacterium kefirresidentii | % Top 5 Species | % Streptococcus salivarius | % Top 5 Species | % Unclassified |
|---|---|---|---|---|---|
| ERR6913124 | 0.0% | 0.0% | 74.5% | ||
| ERR6913124.brackenreport | 21.6% | 38.8% | |||
| ERR6913139 | 1.0% | 14.8% | 23.1% | ||
| ERR6913139.brackenreport | 0.0% | 15.7% | |||
| ERR6913141 | 1.6% | 13.2% | 21.7% | ||
| ERR6913141.brackenreport | 0.0% | 5.2% | |||
| ERR6913143 | 12.6% | 28.2% | 13.5% | ||
| ERR6913143.brackenreport | 0.0% | 30.8% | |||
| ERR6913220 | 0.0% | 0.0% | 9.9% | ||
| ERR6913220.brackenreport | 15.9% | 30.6% | |||
| ERR6913235 | 1.4% | 8.2% | 24.0% | ||
| ERR6913235.brackenreport | 0.1% | 12.1% | |||
| ERR6913237 | 0.4% | 5.3% | 6.2% | ||
| ERR6913237.brackenreport | 0.0% | 2.4% | |||
| ERR6913239 | 6.1% | 17.9% | 11.1% | ||
| ERR6913239.brackenreport | 0.0% | 25.9% |
Bracken
Bracken is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.DOI: 10.7717/peerj-cs.104.
Top taxa
The number of reads falling into the top 5 taxa across different ranks.
To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.
The total number of reads is approximated by dividing the number of unclassified reads by the percentage of
the library that they account for.
Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.
The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.
Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.
Kraken
Kraken is a taxonomic classification tool that uses exact k-mer matches to find the lowest common ancestor (LCA) of a given sequence.DOI: 10.1186/gb-2014-15-3-r46.
Top taxa
The number of reads falling into the top 5 taxa across different ranks.
To make this plot, the percentage of each sample assigned to a given taxa is summed across all samples. The counts for these top 5 taxa are then plotted for each of the 9 different taxa ranks. The unclassified count is always shown across all taxa ranks.
The total number of reads is approximated by dividing the number of unclassified reads by the percentage of
the library that they account for.
Note that this is only an approximation, and that kraken percentages don't always add to exactly 100%.
The category "Other" shows the difference between the above total read count and the sum of the read counts in the top 5 taxa shown + unclassified. This should cover all taxa not in the top 5, +/- any rounding errors.
Note that any taxon that does not exactly fit a taxon rank (eg. - or G2) is ignored.
